Measurement of the internal state of alkali atoms in an atomic clock is typically done using resonance fluorescence. To distinguish between the upper and lower ground states of the atoms, the atoms are probed with light on resonance with the upper ground state but not the lower ground state. Next, an optical repumping step transfers the lower state population to the upper state and the same resonance is used to probe the atoms again. At this point, the fluorescence signal contains a contribution from all of the atoms. If the sample of atoms to be measured is captured from hot vapor in a vapor cell, problems occur when the repumping step repumps all the atoms in the background vapor as well, increasing the overall light level in the second probe, and reducing the size of the signal compared to the background.